Handbrake and VidCoder are two excellent choices, and if you are new to conversions, I’d recommend starting with them.
There are others that have more controls available, like Ripbot264 and MeGUI, but I rarely use them, and then only when I’m making raw .h264 files for Blu-ray authoring.
MakeMKV’s primary weakness with decrypting and ripping DVD’s is the fact that it only outputs to MKV files, but since your eventual target is an mp4 file for an iPod, the MKV file from MakeMKV will work very well as input to Handbrake or VidCoder.
You’ll need to get new beta keys for the program from the MakeMKV forum every month or so: http://www.makemkv.com/forum2/viewtopic.php?f=5&t=1053
If you want another free choice for a modern DVD decryption program, look at TDMore Free DVD Copy: http://www.tdmore.com/free-dvd-copy.html